Checking how variance influences smoothing
XSun
2023-04-11
Last updated: 2023-04-14
Checks: 4 2
Knit directory: /project/xinhe/xsun/mutation_rate/1.exp_obs_gnomad/
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Introduction
Here, we do more investigations to check how variance influences smoothing.
The variances are \(\sigma_{i}^{2}\) from:
\(y_{i} = x_{i} + \varepsilon _{i}\), \(\varepsilon _{i} \sim N(0, \sigma _{i}^{2})\)
In earlier setting, \(\sigma_{i}^{2}\) are different for each window. But in the constant variance setting, the \(\sigma_{i}^{2}\) are the same across all chromosome. \(\sigma_{i}^{2}\) is computed by sd_estimate_gasser_etal(data$log_randeff) from smashr.
1kb
All 6 mutation types
[1] "the current constant variance is 0.299329381569965"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.897988144709894we have"
[1] "If we set the variance larger, as current constant variance *8 = 2.39463505255972we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0997764605233216we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0374161726962456we have"
Hot spots (22.5Mb - 23.5Mb)
[1] "the variance in current window"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.897988144709894we have"
[1] "If we set the variance larger, as current constant variance *8 = 2.39463505255972we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0997764605233216we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0374161726962456we have"
Cold spots (21Mb - 22Mb)
[1] "the variance in current window"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.897988144709894we have"
[1] "If we set the variance larger, as current constant variance *8 = 2.39463505255972we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0997764605233216we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0374161726962456we have"
Cold spots (18Mb - 19Mb)
[1] "the variance in current window"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.897988144709894we have"
[1] "If we set the variance larger, as current constant variance *8 = 2.39463505255972we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0997764605233216we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0374161726962456we have"
typical regions (25Mb - 26Mb)
[1] "the variance in current window"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.897988144709894we have"
[1] "If we set the variance larger, as current constant variance *8 = 2.39463505255972we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0997764605233216we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0374161726962456we have"
typical regions (31Mb - 32Mb)
[1] "the variance in current window"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.897988144709894we have"
[1] "If we set the variance larger, as current constant variance *8 = 2.39463505255972we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0997764605233216we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0374161726962456we have"
10kb
All 6 mutation types
[1] "the current constant variance is 0.224604191106067"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.6738125733182we have"
[1] "If we set the variance larger, as current constant variance *8 = 1.79683352884853we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0748680637020222we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0280755238882583we have"
Hot spots (22.5Mb - 23.5Mb)
[1] "the variance in current window"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.6738125733182we have"
[1] "If we set the variance larger, as current constant variance *8 = 1.79683352884853we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0748680637020222we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0280755238882583we have"
Cold spots (21Mb - 22Mb)
[1] "the variance in current window"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.6738125733182we have"
[1] "If we set the variance larger, as current constant variance *8 = 1.79683352884853we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0748680637020222we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0280755238882583we have"
Cold spots (18Mb - 19Mb)
[1] "the variance in current window"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.6738125733182we have"
[1] "If we set the variance larger, as current constant variance *8 = 1.79683352884853we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0748680637020222we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0280755238882583we have"
typical regions (25Mb - 26Mb)
[1] "the variance in current window"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.6738125733182we have"
[1] "If we set the variance larger, as current constant variance *8 = 1.79683352884853we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0748680637020222we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0280755238882583we have"
typical regions (31Mb - 32Mb)
[1] "the variance in current window"
[1] "the log(random effect) using default setting:"
[1] "the log(random effect) using constant variance:"
[1] "If we set the variance larger, as current constant variance *3 = 0.6738125733182we have"
[1] "If we set the variance larger, as current constant variance *8 = 1.79683352884853we have"
[1] "If we set the variance smaller, as current constant variance *1/3 = 0.0748680637020222we have"
[1] "If we set the variance smaller, as current constant variance *1/8 = 0.0280755238882583we have"
sessionInfo()R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.4 (Ootpa)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el8-x86_64/lib/libopenblas_skylakexp-r0.3.13.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] smashr_1.2-9 data.table_1.14.4 gridExtra_2.3 ggplot2_3.4.2
loaded via a namespace (and not attached):
[1] wavethresh_4.6.9 tidyselect_1.2.0 xfun_0.38 bslib_0.3.1
[5] ashr_2.2-54 lattice_0.20-45 colorspace_2.0-3 vctrs_0.6.1
[9] generics_0.1.2 htmltools_0.5.2 yaml_2.3.5 utf8_1.2.2
[13] rlang_1.1.0 mixsqp_0.3-48 jquerylib_0.1.4 later_1.3.0
[17] pillar_1.9.0 glue_1.6.2 withr_2.5.0 lifecycle_1.0.3
[21] stringr_1.4.0 munsell_0.5.0 gtable_0.3.0 workflowr_1.7.0
[25] caTools_1.18.2 evaluate_0.15 labeling_0.4.2 knitr_1.39
[29] fastmap_1.1.0 httpuv_1.6.5 invgamma_1.1 irlba_2.3.5
[33] fansi_1.0.3 highr_0.9 Rcpp_1.0.9 promises_1.2.0.1
[37] scales_1.2.0 jsonlite_1.8.0 truncnorm_1.0-8 farver_2.1.0
[41] fs_1.5.2 digest_0.6.29 stringi_1.7.6 dplyr_1.1.1
[45] grid_4.2.0 rprojroot_2.0.3 cli_3.6.1 tools_4.2.0
[49] bitops_1.0-7 magrittr_2.0.3 sass_0.4.1 tibble_3.2.1
[53] pkgconfig_2.0.3 MASS_7.3-58.3 Matrix_1.5-3 SQUAREM_2021.1
[57] rmarkdown_2.14 rstudioapi_0.13 R6_2.5.1 git2r_0.30.1
[61] compiler_4.2.0